Tuesday, May 8, 2012

Here is How Evolutionists Are Trying To Account For Adaptive Mutations

It has long been known, and even longer been suspected, that organisms not only can adapt rapidly to environmental challenges, but that such adaptations can be passed on to subsequent generations. Evolutionists have resisted such findings, but they now are beyond dispute. Whereas the evolutionary dogma had been that populations undergo change via selection acting on random variation, the science revealed that populations can change quite rapidly and in response to the environmental shift. Indeed there are is a variety of mechanisms that are now at least partially understood that play a role in this environmentally-directed process. Some influence which genes are expressed and others modify the DNA using the so-called adaptive mutations. So now at least some evolutionists are trying to incorporate this once eschewed view into evolutionary theory. Here is a paper that gives a brief overview of the idea that evolution has created a complex set of mechanisms which, in turn, produce these directed adaptations that we observe in biology. It begins by noting that a few leading evolutionists had a sense that random mutations plus natural selection were insufficient to explain the biological world, and how they were correct:

even [August] Weismann, the father of neo-Darwinism, decided late in his career that directed variation must be invoked to understand some phenomena, as random variation and selection alone are not a sufficient explanation. This minireview will describe mechanisms of mutation that are not random and can accelerate the process of evolution in specific directions. The existence of such mechanisms has been predicted by mathematicians who argue that, if every mutation were really random and had to be tested against the environment for selection or rejection, there would not have been enough time to evolve the extremely complex biochemical networks and regulatory mechanisms found in organisms today. Dobzhansky expressed similar views by stating “The most serious objection to the modern theory of evolution is that since mutations occur by ‘chance’ and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye.”

The paper next introduces the idea that environmental stress causes directed feedback mechanisms to accelerate adaptation. The idea is that these mechanisms work together to expose DNA segments to mutations.

Many scientists may share Dobzhansky's intuitive conviction that the marvelous intricacies of living organisms could not have arisen by the selection of truly random mutations. This minireview suggests that sensitive, directed feedback mechanisms initiated by different kinds of stress might facilitate and accelerate the adaptation of organisms to new environments. The specificity in the series of events summarized by Fig. 3 resides entirely in the first step, which is meant to suggest a pattern of derepression elicited by a corresponding pattern of adverse conditions. Microorganisms in nature must be confronted simultaneously by a complex set of problems, for example, the threat of oxidative or osmotic damage together with suboptimum concentrations of many essential nutrients. Transcriptional activation of genes derepressed to various degrees would expose the nontranscribed strands to mutations and stimulate localized supercoiling. Vulnerable bases in the complex DNA structures resulting from supercoiled DNA will also contribute to localized hypermutation in the genes activated to cope with the stresses that initiate the above series of events.

So the idea is that that the environment not only creates life, but it continues to direct evolution by fine-tuning the DNA copying process. After all, organisms that can respond more effectively to environmental challenges would have an obvious advantage:

The environment gave rise to life and continues to direct evolution. Environmental conditions are constantly controlling and fine-tuning the transcriptional machinery of the cell. Feedback mechanisms represent the natural interactive link between an organism and its environment. An obvious selective advantage exists for a relationship in which particular environmental changes are metabolically linked through transcription to genetic changes that help an organism cope with new demands of the environment. 

In other words, evolution does not merely occur by random events. It occurs via complex mechanisms which evolution first created. This work demonstrates how robust evolutionary theory is to falsified predictions. It also demonstrates the immense level of serendipity in evolutionary theory.

28 comments:

  1. mutations with selection plus time ain't enough after all say some of the boys!!
    Creationists knew that already!
    They are just so desperate to explain nature without Gods fingerprints or even thumbs up.

    If mutations is not good enough and this is a credible conclusion then they can't complain when creationists say it !
    We were just ahead of the pack!
    Will this now be taught in schools?
    Is it scientific to say mutations is not good enough or was it ever scientific to say they were?
    Is this a paradigm shift?

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  2. It's a fascinating paper, Cornelius, but you miss so much fun in simply skimming it for evidence that our prior conceptions of evolutionary mechanisms are wrong.

    As the author says:

    In a scientific context, the word spontaneous is meaningless. Every event is preceded by, and dependent upon, innumerable known and unknown prior events and circumstances.

    For "spontaneous" read "random".

    "Random" is a shorthand for "we cannot make a predictive generalization".

    If it turns out, in the case of mutations, that we can, cool.

    But note:

    As will become apparent, genetic derepression may be the only mechanism by which particular environmental conditions of stress target specific regions of the genome for higher mutation rates (hypermutation). Although this direct avenue for increasing variability is probably not available to multicellular organisms in which germ cells and somatic cells are separated, the derepression of biosynthetic pathways is essential to increased longevity in mammals subjected to caloric restriction (54), and amino acid limitation in rats can also induce gene expression (9)

    But yes, evolvability can clearly evolve. There's nothing paradigm-shifting in that.

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    1. 'There's nothing paradigm-shifting in that.'

      Nothing to see here, Move along; - video
      http://www.youtube.com/watch?v=rSjK2Oqrgic

      Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009
      Excerpt (Page 12): Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents.,,, Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
      http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

      Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

      Seeing Past Darwin II: James A. Shapiro - James Barham - May 2012
      Excerpt: Much in our culture depends upon the public’s being made aware that Darwinian theory as standardly interpreted is intellectually bankrupt.(2) And little that I have encountered communicates this fact so well as the work of James A. Shapiro.
      http://www.thebestschools.org/bestschoolsblog/2012/05/03/darwin-ii-james-a-shapiro/

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    2. Cornelius Hunter

      No Ian, you are simply providing yet another great example of how evolution harms science. It's dogma has gone viral and doesn't allow the scientific facts to get out.


      So CH, is this one of those scientific facts that evolution doesn't allow to get out?

      They sure did a good job of hiding it by publishing it in a well read, high impact factor, publicly available journal, didn't they?

      What other scientific facts has evolution not allowed to get out? Please list the major ones, the ones you obviously had in mind when you made that remarkable claim.

      All those who look to you for scientific enlightenment thank you in advance.

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    3. Elizabeth,

      Not true. We can make a predictive generalisation for an inherently stochastic phenomenon. This is the subject of statistics. At quantum level reality is stochastic and yet science works for the exact same reason that we can make generalisations.

      That's what I have always disliked about unguided evolution: it asserts "sometimes A happens" and "sometimes A does not happen" at the same time. These conditions are obscure and they are getting more obscure over time as we collect more data. Divergent vs convergent evolution, mutations vs neutral evolution, epigenetic factors, etc. The original beautiful looking theory is so ugly and fat now that I guess even Darwin himself could not qualify for being a true Darwinist, especially since no one really knows what it means to be one.

      It is time we shifted the paradigm. It is time we recognised teleology.

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    4. Aftermath: Not true. We can make a predictive generalisation for an inherently stochastic phenomenon. This is the subject of statistics. At quantum level reality is stochastic and yet science works for the exact same reason that we can make generalisations.

      Yes, I know. But that does not invalidate my point.

      The original beautiful looking theory is so ugly and fat now that I guess even Darwin himself could not qualify for being a true Darwinist, especially since no one really knows what it means to be one.

      Darwin would certainly be amazed, and his theory has indeed grown fat, but certainly not ugly.

      As for "no one really knows what it means to be one" - sure. I never know what "Darwinist" is even supposed to mean. I just describe myself as one who subscribes to the evolving framework that describes the story of life on earth, and is broadly called "evolutionary theory".

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    5. It seems to me that you're making all sorts of unwarranted assumptions about designers, in that they are skinny, rather than fat.

      Not to mention that if "A designer did it" is skinny, then why isn't it preferred in all cases?

      Specifically, if you assume the existence of a inexplicable supernatural realm that surrounds a bubble of explicably, there can be no better explanation in this inexplicable realm but "Zeus rules" there.

      However, if this sea of inexplicability supposedly reaches in to effect the inside of this bubble, such as to design organisms, there can be no better explanation than "Zeus rules" here as well, as it could affect anything in an inexplicable way.

      In other words, the idea that the inside of this bubble is explicable would be an illusion which could only be maintain by carefully avoiding specific questions.

      For example, what if a supernatural designer wanted to create the world we observe thirty seconds ago using some inexplicable means for some inexplicable reason? If this was the case, then you wouldn't have authored the comment I'm responding to. Rather, this supernatural being would have authored it using inexplicable means for some inexplicable reason.

      One could do this with pretty much anything, which makes it an appeal to one of many general purpose means of deny anything.

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  4. Elizabeth Liddle said
    "But yes, evolvability can clearly evolve. There's nothing paradigm-shifting in that."

    It is not only evolved evolvability, it is a mechanism for increase evolvability as response of enviromental changes. So, not ramdom mutations to the needs but a mechanism that allows to chnge when needed. If you cannot see a paradigm-shifting there is because ToE fit at any paradigm.

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  5. Yes, adaptive mutations. If x, then y, else z. If a, then b, else c... and so on. Planned, intelligent and bounded change. Any questions?

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  6. I forgot to add- the living cell possesses artifical intelligence. The 21st century will not play nice with Darwinism.

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  7. Neal,

    Before a cell could adapt it would need to possess the knowledge of under which scenarios it should adapt, the knowledge of which specific adaptation to employ and the knowledge of how to build that adaptation in particular. Right?

    So, the question is, what is the origin of this knowledge. How was it created?

    Again, a designer that "just was", complete with the knowledge of when, which and how adaptation should be made, already present, doesn't serve an explanatory purpose. This is because one could more economically state that organisms "just appeared", complete with the knowledge of when, which and how adaptations should be made.

    In other words, "A designer did it." doesn't actually explain anything. All you've done is push the problem into some inexplicable realm, then claimed you've solved it.

    Do you have any criticism of this? Does anyone have any criticism of this?

    Given that you keep repeating this same claim over and over again, it appears that you either do not understand how "A designer did it." fails as an explanation or you fail to recognize "A designer did it." as an idea that should be subject to criticism.

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  8. If people observe an evolutionary event, it can't be said to be proof of Darwinism because maybe it was the result of a pre-existing mechanism. It looks like the the evidence for Darwinism is getting weaker and weaker.

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  9. Nat,

    How would you tell the difference, what evidence is for each?

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  10. Scott,

    First, your usage of the word "knowledge" is not standard. It is normally related to cognition.

    Second, saying "a designer did it" is not a dead end road. You're misrepresenting this position. The design view is inspiring and liberating to look deeper under the hood to research function and how it was put together. We have historical presidence for great discoveries being done by those that held to the design view. Your argument is a canard. It is the evolutionists who are shackled to a worldview that stiffles freedom and forces them to hunker down and stretch their claims beyond the evidence.

    The objective nested hierarchy has been invalidated by the data, let's talk about that for awhile. Can evolution survive without the objective nested hierarchy?

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    1. Neal : First, your usage of the word "knowledge" is not standard. It is normally related to cognition.

      Yet I've been very clear as to what is meant when I use the term. As such, it's unclear how this "criticism" of the explanation itself. In case it's not clear...

      While they both have many functions, Human brains and DNA are both represent general purpose information storage media. Once embodied there, information tends to remain there in a suitable environment, which is what I refer to when I use the term knowledge.

      Furthermore, there are two kinds of knowledge: non-explanatory and explanatory. Biological systems represent non-explanatory knowledge, which is limited in it's reach. People, on the other hand, can create explanatory knowledge, which can have broad and even unlimited reach. This is because people are universal explainers.

      So, now that we've cleared this up, do you actually have any criticism of the explanation itself?

      Neal: The design view is inspiring and liberating to look deeper under the hood to research function and how it was put together.

      So, the purpose of ID is to be inspiring? But that's not an explanatory purpose in regards to biological adaptations. Nor would it be necessary to actually perform any research since one could more economically state that organisms, "just appeared", complete with the knowledge of how to build their adaptations, already present. Why bother?

      Again, you still seem to be confused as to how ID fails as an explanation since it fails to explain the origin of the knowledge used by the supposed designer.

      Neal: We have historical presidence for great discoveries being done by those that held to the design view.

      Except, none of their discoveries actually depend upon the design view being true. They stand on their own as explanations. Nor do we talk of Muslim algebra or Christian physics. In other words, science is no longer based on natural theology.

      Rather, we explain our relatively recent, rapid increate in the creation of knowledge in that progress comes from criticizing explanations. Specifically, good explanations are deep and hard to vary, while bad expansions are shallow and easily varied.

      Neal: The objective nested hierarchy has been invalidated by the data, let's talk about that for awhile. Can evolution survive without the objective nested hierarchy?

      Even Darwin new about hybridization. Nor do we assume any theory is exhaustively true or complete. For example, there are mechanisms that we have yet to discover yet. Evolution would predict that these mechanism will represent a form of genetic conjecture and refutation that creates non-explanatory knowledge, just as horizontal gene transfer and common decent.

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  11. Nat: If people observe an evolutionary event, it can't be said to be proof of Darwinism because maybe it was the result of a pre-existing mechanism.

    Nat, perhaps you'll be the one to answer my question.

    Are dinosaurs merely an interpretation of our best explanation of fossils? Or are they *the* explanation for fossils?

    After all, there are an infinite number of rival interpretations that accept the same evidence, yet suggest that dinosaurs never existed millions of years ago.

    For example, there is the rival interpretation that fossils only come into existence when they are consciously observed. Therefore, fossils are no older than human beings. As such, they are not evidence of dinosaurs, but evidence of acts of those particular observations.

    Another interpretation would be that dinosaurs are such weird animals that conventional logic simply doesn't apply to them. This is the same sort of reasoning that suggests human consciousness is so unique that determinism simply doesn't apply to it.

    One could suggests It's meaningless to ask if dinosaurs were real or just a useful fiction to explain fossils.

    Not to mention the rival interpretation that designer chose to create the world we observe 30 second ago. Therefore, dinosaurs couldn't be the explanation for fossils, because they didn't exist until 30 seconds ago.

    In other words, "maybe it was the result of" could be applied to anything, including fossils, whether you actually wrote the comment I'm responding to, etc. This isn't unique to evolutionary theory.

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    1. It seems to me that dinosaurs are one explanation for the fossils. But even if they are the best explanation there are other explanations besides evolution for dinosaurs.

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    2. Nat: But even if they are the best explanation there are other explanations besides evolution for dinosaurs.

      But, as I pointed out, there are also an infinite number of rival interpretations of fossils as well. Why isn't this a problem for dinosaurs as well?

      For example, couldn't some designer have modified fossils using some incomprehensible means for an incomprehensible reason?

      So, to reiterate, are dinosaurs merely an interpretation of our best explanation of fossils? If, not why?

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    3. Dinosaurs are probabsly the best interpretation, but evolution is not the only, or even the best interperation of dinosaurs.

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    4. natschuster

      Dinosaurs are probabsly the best interpretation, but evolution is not the only, or even the best interperation of dinosaurs.


      Tell us nat, what *is* he best interpretation of the geographic, morphological, and temporal distribution of dinosaur fossils in the fossil record?

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    5. It seems to me that the best interpretation of the distribution of fossils is a series of creation and destruction events as per several theologies,

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    6. Nat: Dinosaurs are probabsly the best interpretation, but evolution is not the only, or even the best interperation of dinosaurs.

      That's what you said earlier. This is no clearer no then it was then.

      Again, notice that we do not speak of dinosaurs as merely our best interpretation of our best theory of fossils. Yet, there are an infinite number of rival interpretations that accept the same evidence, yet suggest that dinosaurs never existed millions of years ago. Nor is the theory primarily about fossils, but about dinosaurs.

      In other words, does the fact that we do not speak of dinosaurs as merely an interpretation of our our best explanations of fossils represent a misrepresentation of science?

      Nat: It seems to me that the best interpretation of the distribution of fossils is a series of creation and destruction events as per several theologies,

      Evasive much?

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    7. Scott:

      Maybe I don't understand the question. There are lots of explanation for dinosaur fossils, true. I was under the impression that you were asking me for my opinion of the best one.

      And yes, I do believe that if scientists insist that the only interpretation of fossils is dinosaurs then that is a misrepresentation of the truth. Whether it is a misrepresentation of science depends on your definition of science.

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    8. Nat: Maybe I don't understand the question. There are lots of explanation for dinosaur fossils, true.

      It would seem so. Let's start from the beginning...

      We do not speak of dinosaurs as merely an interpretation of our best explanation of fossils. Is this true or false?

      And, by interpretation, I'm specifically referring to one of the components of a scientific theory: formalisms, observations and interpretations.

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    9. I"m under the imprssion that dinosaurs are considered the only scientific explanation.

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    10. Nat,

      Interpretations can be infinitely varied to accept the same empirical observations, yet suggest something completely different is happening in reality. This includes dinosaurs never having existed millions of years ago, while accepting the same observations of fossils.

      This infinite variability is why science isn't merely interpretations alone. Rather, it's explanations, which represent all aspects of a theory - formalism, observations and interpretations - as a coherent whole for the purpose of criticism. They depend on each other.

      If they didn't depend on each other, it wouldn't be possible to make progress as there would be an infinite number of interpretations which could not be criticized.

      Again, this is why we do not speak of dinosaurs as merely an interpretation of our best theory of fossils. Rather, we say dinosaurs are the explanation of fossils. It's also why the explanation is primarily about dinosaurs, rather than fossils, despite fossils being the "things" being observed.

      However, Cornelius wants to depict empirical observations as being independent of interpretations, in that they are not part of a coherent whole. But as I've illustrated, there are an infinite number of interpretations can result in significantly different assumptions about reality - despite accepting the same same empirical observations.

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  12. Recently Cornelius posted evidence of the lies and fraud done by evolutionists surrounding the Scopes trial. One would wonder if they could go any lower. Well, they did...

    "You can be a brilliant, innovative pediatric neurosurgeon at a sky-scraping top medical school, in addition to being a generous philanthropist with an inspirational up-from-dire-poverty personal story, plus a Presidential Medal of Freedom winner, and a best-selling writer whose memoir was turned into a TV movie starring Cuba Gooding Jr.

    All that, but if you once shared your critical thoughts on evolutionary science and its moral implications -- everything else about you suddenly dwindles to very little.

    Dr. Ben Carson of Johns Hopkins University is that man. He's scheduled to give the Commencement address and receive an honorary degree at Emory University but close to 500 faculty members, students and staff protested, drawing up a gravely serious letter to the student paper expressing their "concerns." Over what? Carson had no intention of speaking about evolution but someone dug up an impromptu interview he once gave to a publication associated with his Christian denomination (he's a Seventh Day Adventist)."

    http://www.evolutionnews.org/2012/05/intimidating_da059401.html

    The movie, "Gifted Hands" is based on his story.

    500 faculty members, students and staff protested. Seriously?

    The hogwash mill of evolution is still going strong.

    They absolutely hate someone of Dr Carson's record being an inspiration to future scientists and doctors. What a nerve has for doing ground breaking medical work without bowing to evolution.

    They can't stand it that their god does not get credit for it... "we ask you to also consider the enormous positive impact of science on our lives and how that science rests squarely on the shoulders of evolution."

    Another gem from their letter.."Dr. Carson insists on not seeing a difference between science, which is predictive and falsifiable, and religious belief systems, which by their very nature cannot be falsified."

    Evolution is predictive and falsifiable? What world are they living in?

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